Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c45feb9..d32ff46 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -34,7 +34,9 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
@@ -56,7 +58,6 @@ import javax.help.HelpSetException;
 import javax.swing.JColorChooser;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
@@ -291,12 +292,16 @@ public class Preferences extends GPreferences
     /*
      * Set Colours tab defaults
      */
-    for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+    protColour.addItem(ResidueColourScheme.NONE);
+    nucColour.addItem(ResidueColourScheme.NONE);
+    for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
     {
-      protColour.addItem(ColourSchemeProperty.getColourName(i));
-      nucColour.addItem(ColourSchemeProperty.getColourName(i));
+      String name = cs.getSchemeName();
+      protColour.addItem(name);
+      nucColour.addItem(name);
     }
-    String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+    String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+            ResidueColourScheme.NONE);
     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
@@ -689,12 +694,7 @@ public class Preferences extends GPreferences
   {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser.forRead(
-            Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
-    // new String[] {
-    // "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-    // "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
-    // "PIR", "BLC", "Jalview" },
-    // fileFormat);
+            Cache.getProperty("LAST_DIRECTORY"), fileFormat);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.select_startup_file"));
@@ -707,7 +707,7 @@ public class Preferences extends GPreferences
       if (format != null)
       {
         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
-                format.toString());
+                format.getName());
       }
       startupFileTextfield.setText(chooser.getSelectedFile()
               .getAbsolutePath());
@@ -761,9 +761,9 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -788,10 +788,10 @@ public class Preferences extends GPreferences
     int index = linkNameList.getSelectedIndex();
     if (index == -1)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.no_link_selected"),
               MessageManager.getString("label.no_link_selected"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
 
@@ -802,9 +802,9 @@ public class Preferences extends GPreferences
     while (!valid)
     {
 
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -828,10 +828,10 @@ public class Preferences extends GPreferences
     int index = linkNameList.getSelectedIndex();
     if (index == -1)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.no_link_selected"),
               MessageManager.getString("label.no_link_selected"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
     nameLinks.removeElementAt(index);
@@ -923,10 +923,10 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -949,10 +949,10 @@ public class Preferences extends GPreferences
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
-                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.ERROR_MESSAGE);
         return false;
       }
     }
@@ -988,13 +988,13 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JOptionPane.showInternalOptionDialog(
+      int showHelp = JvOptionPane.showInternalOptionDialog(
               Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
               null, options, options[0]);
-      if (showHelp == JOptionPane.NO_OPTION)
+      if (showHelp == JvOptionPane.NO_OPTION)
       {
         try
         {